Tag: kegg

Job – Principal Biostistician/Bioinformatics job at Kenya Medical Research

Vacancy title: Principal Biostistician/Bioinformatics [ Type: FULL TIME , Industry: Research , Category: Research ] Jobs at: Kenya Medical Research – KEMRI Deadline of this Job: 06 October 2022   Duty Station: Within Kenya , Kisumu , East Africa SummaryDate Posted: Tuesday, September 20, 2022 , Base Salary: Not Disclosed…

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KEGG COMPOUND: C00236

KEGG COMPOUND: C00236     COMPOUND: C00236 Help Entry C00236                      Compound                                Name 3-Phospho-D-glyceroyl phosphate;1,3-Bisphospho-D-glycerate;(R)-2-Hydroxy-3-(phosphonooxy)-1-monoanhydride with phosphoric propanoic acid;D-Glycerate 1,3-diphosphate Formula C3H8O10P2 Exact mass 265.9593 Mol weight 266.0371 Structure Mol fileKCF fileDB search Reaction Pathway map00010   Glycolysis / Gluconeogenesis map00710   Carbon fixation in photosynthetic organisms map01060   Biosynthesis of plant secondary metabolites map01061   Biosynthesis…

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KEGG ORTHOLOGY: K17753

KEGG ORTHOLOGY: K17753     ORTHOLOGY: K17753 Help Entry K17753                      KO                                      Symbol HICDH Name isocitrate–homoisocitrate dehydrogenase [EC:1.1.1.286] Pathway map01110   Biosynthesis of secondary metabolites map01120   Microbial metabolism in diverse environments map01210   2-Oxocarboxylic acid metabolism Brite KEGG Orthology (KO) [BR:ko00001] 09100 Metabolism  09101 Carbohydrate metabolism   00020 Citrate cycle (TCA cycle)    K17753  HICDH; isocitrate–homoisocitrate dehydrogenase  09105 Amino acid metabolism   00300 Lysine biosynthesis    K17753  HICDH;…

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KEGG COMPOUND: C00509

KEGG COMPOUND: C00509     COMPOUND: C00509 Help Entry C00509                      Compound                                Name Naringenin;4′,5,7-Trihydroxyflavanone;(2S)-Naringenin;(-)-(2S)-Naringenin Formula C15H12O5 Exact mass 272.0685 Mol weight 272.2528 Structure Mol fileKCF fileDB search Reaction Pathway map01061   Biosynthesis of phenylpropanoids map01110   Biosynthesis of secondary metabolites Module M00137   Flavanone biosynthesis, phenylalanine => naringenin M00138   Flavonoid biosynthesis, naringenin => pelargonidin M00941   Isoflavone…

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Data Scientist – Bioinformatics at Faculty – London, England, United Kingdom

Faculty is one of Europe’s leading applied artificial intelligence companies. We build, deploy and operate AI solutions to increase our customers’ performance and help them realise their full potential. We believe that AI should be trustworthy, impactful and beneficial across society. Those principles have shaped our work with more than…

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KEGG T01001: 4171

Entry 4171              CDS       T01001                                  Symbol MCM2, BM28, CCNL1, CDCL1, D3S3194, DFNA70, MITOTIN, cdc19 Name (RefSeq) minichromosome maintenance complex component 2   KO K02540   DNA replication licensing factor MCM2 [EC:5.6.2.3] Organism hsa  Homo sapiens (human) Pathway hsa03030   DNA replication hsa04110   Cell cycle Disease H00604   Deafness, autosomal dominant Brite KEGG Orthology (KO) [BR:hsa00001] 09120 Genetic Information Processing  09124…

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KEGG T02666: 101290786

Entry 101298727         CDS       T02666                                  Name (RefSeq) triacylglycerol lipase SDP1   KO K14674   TAG lipase / steryl ester hydrolase / phospholipase A2 / LPA acyltransferase [EC:3.1.1.3 3.1.1.13 3.1.1.4 2.3.1.51] Organism fve  Fragaria vesca (woodland strawberry) Pathway fve00100   Steroid biosynthesis fve00561   Glycerolipid metabolism fve00564   Glycerophospholipid metabolism fve00565   Ether lipid metabolism fve00590   Arachidonic acid metabolism fve00591   Linoleic…

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Bioinformatics Analysis of the Key Genes and Pathways in Multiple Myel

Introduction Multiple myeloma is a B-cell malignancy characterized by the malignant proliferation of clonal plasma cells in bone marrow,1 It is the second most common hematological malignancy after lymphoma.2 The age-standardised rate (ASR) of multiple myeloma incidence was 1·78 (95% UI 1·69-1·87) per 100 000 people globally and mortality was…

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KEGG COMPOUND: C03793

KEGG COMPOUND: C03793     COMPOUND: C03793 Help Entry C03793                      Compound                                Name N6,N6,N6-Trimethyl-L-lysine Formula C9H20N2O2 Exact mass 188.1525 Mol weight 188.2673 Structure Mol fileKCF fileDB search Reaction Pathway Enzyme Other DBs KCF data Show ATOM        13            1   N1d N    30.1000  -20.2300 #+            2   C1b C    28.9100  -20.9300            3   C1a C    31.2900  -20.9300            4   C1a C    30.1000  -18.8300            5   C1a C    29.8200  -21.8400            6   C1b C    27.6500  -20.2300            7   C1b C    26.4600  -20.9300            8   C1b C    25.2700  -20.2300            9   C1c C    24.0100  -20.9300            10  C6a C    22.8200  -20.2300            11  N1a N    24.0100  -22.3300            12  O6a O    22.8200  -18.8300            13  O6a O    21.4900  -20.8600 #-BOND        12            1     1   2 1            2     1   3 1            3     1   4…

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KEGG COMPOUND: C17729

KEGG COMPOUND: C17729     COMPOUND: C17729 Help Entry C17729                      Compound                                Name Nicofetamide;N-(1,2-Diphenylethyl)nicotinamide Formula C20H18N2O Exact mass 302.1419 Mol weight 302.3697 Structure Mol fileKCF fileDB search Remark Brite Anatomical Therapeutic Chemical (ATC) classification [BR:br08303] A ALIMENTARY TRACT AND METABOLISM  A03 DRUGS FOR FUNCTIONAL GASTROINTESTINAL DISORDERS   A03A DRUGS FOR FUNCTIONAL GASTROINTESTINAL DISORDERS    A03AC Synthetic antispasmodics, amides with…

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Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma | BMC Medical Genomics

Sia D, Tovar V, Moeini A, Llovet JM. Intrahepatic cholangiocarcinoma: pathogenesis and rationale for molecular therapies. Oncogene. 2013;32(41):4861–70. CAS  Article  Google Scholar  Sungwan P, Lert-Itthiporn W, Silsirivanit A, Klinhom-On N, Okada S, Wongkham S, Seubwai W. Bioinformatics analysis identified CDC20 as a potential drug target for cholangiocarcinoma. PeerJ. 2021;9:e11067. Article …

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Acute phase of ischemia-reperfusion in rats

Introduction Stroke is one of the leading causes of death and disability worldwide, which causes substantial economic and social burdens.1 Ischemic stroke is caused by insufficient blood and oxygen supply to the brain,2 accounting for about 85% of the casualties of stroke patients.3 The concept of treatment for ischemic injury…

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CRISPRa screen identifies a role for c-KIT signaling in tamoxifen resistance, potentially through upregulation of ABC transporters

Abstract Resistance to endocrine therapy is a common problem in patients with estrogen receptor alpha (ERα) positive breast cancer. In this study, we took a non-biased genome-wide approach to identify novel mechanisms of endocrine resistance using a clustered regularly interspaced short palindromic repeats (CRISPR) activating (CRISPRa) screen. Results from the…

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uniprot – How to annotate list of proteins with KEGG orthology groups?

I’ve got a list of proteins, complete with Uniprot IDs. I’d like to group them into orthology groups based on data from KEGG, but I have no idea how to add a column with KEGG groups. I’ve tried poking around in the documentation for UniProt, but all I can find…

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KEGG REACTION: R11822

KEGG REACTION: R11822     REACTION: R11822 Help Entry R11822                      Reaction                                Name (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (+)-isoafricanol-forming] Definition trans,trans-Farnesyl diphosphate + H2O <=> (+)-Isoafricanol + Diphosphate Equation Enzyme Other DBs LinkDB All DBs DBGET integrated database retrieval system Read more here: Source link

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Transcription-independent regulation of STING activation and innate immune responses by IRF8 in monocytes

Reagents, antibodies, viruses and cells LMW-Poly(I:C), LPS, 2′3′-cGAMP and DMXAA (InvivoGen); hydroxyurea, camptothecin and mitomycin C (MCE); GM-CSF, Flt3L (peproTech); lipofectamine 2000 (Invitrogen); polybrene (Millipore); RNAiso Plus (Takara); HT-DNA (Sigma); SYBR (BIO-RAD); dual-specific luciferase assay kit (Promega); ELISA kit for murine Ifn-β (PBL); ELISA kits for murine IP-10 (Biolegend) were…

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KEGG ENZYME: 6.2.1.11

KEGG ENZYME: 6.2.1.11     ENZYME: 6.2.1.11 Help Entry EC 6.2.1.11                 Enzyme                                  Name biotin—CoA ligase;biotinyl-CoA synthetase;biotin CoA synthetase;biotinyl coenzyme A synthetase Class Ligases;Forming carbon-sulfur bonds;Acid-thiol ligasesBRITE hierarchy Sysname biotin:CoA ligase (AMP-forming) Reaction(IUBMB) ATP + biotin + CoA = AMP + diphosphate + biotinyl-CoA [RN:R01075] Reaction(KEGG) Substrate Product History EC 6.2.1.11 created 1972 Pathway…

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In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states

Animals and sample preparation Animal experiments were performed as previously described12. C57BL/6J WT mice or ob/ob mice at ten weeks of age were purchased from Japan SLC Inc. (Shizuoka, Japan). The phenotypic data of the mice are summarized in Table S1. Animal experiments were approved by the animal ethics committee…

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KEGG ENZYME: 3.6.1.39

KEGG ENZYME: 3.6.1.39     ENZYME: 3.6.1.39 Help Entry EC 3.6.1.39                 Enzyme                                  Name thymidine-triphosphatase;thymidine triphosphate nucleotidohydrolase;dTTPase;deoxythymidine-5′-triphosphatase Class Hydrolases;Acting on acid anhydrides;In phosphorus-containing anhydridesBRITE hierarchy Sysname dTTP nucleotidohydrolase Reaction(IUBMB) dTTP + H2O = dTDP + phosphate [RN:R02095] Reaction(KEGG) Substrate Product Comment Also acts, more slowly, on dUTP and UTP. History EC 3.6.1.39 created 1984…

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KEGG REACTION: R00134

Entry R00134                      Reaction                                Name formate:NADP+ oxidoreductase Definition Formate + NADP+ <=> CO2 + NADPH + H+ Equation Reaction class Enzyme Pathway rn00720   Carbon fixation pathways in prokaryotes rn01120   Microbial metabolism in diverse environments Module M00377   Reductive acetyl-CoA pathway (Wood-Ljungdahl pathway) Orthology Other DBs LinkDB All DBs Read more here: Source link

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KEGG T01015: 107278078

Entry 4330855           CDS       T01015                                  Name (RefSeq) auxin-responsive protein SAUR32   KO K14488   SAUR family protein Organism osa  Oryza sativa japonica (Japanese rice) (RefSeq) Pathway osa04075   Plant hormone signal transduction Brite KEGG Orthology (KO) [BR:osa00001] 09130 Environmental Information Processing  09132 Signal transduction   04075 Plant hormone signal transduction    4330855 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam:  Auxin_inducible Motif Other DBs…

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Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants

Volatile fatty acid production and absorption is modulated by diet Animals were adapted to a starch-rich diet by gradually increasing dietary concentrate content from 50 to 90% over the three 100-d experimental periods (Fig. 1A). With both diets, rumen structure and epithelial morphology were robust and rumen pH remained above 6.0…

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Targeted inhibition of ubiquitin signaling reverses metabolic reprogramming and suppresses glioblastoma growth

Cell culture Human glioblastoma cells (U87MG and U87MG-Luc) and human embryonic kidney cells (HEK293) were obtained from the American Type Culture Collection (Manassas, Va.). Cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (Gibco™ Fetal Bovine Serum South America, Thermo Scientific Fisher-US), 2 mM l-glutamine, 50 U/ml…

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Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

Sampling the radiation To understand the phylogenetic relationships between Alpine whitefish, we carried out whole-genome resequencing on 96 previously collected whitefish (with associated phenotypic measurements including standard length and gill-raker counts; collected in accordance with permits issued by the cantons of Zurich (ZH128/15), Bern (BE68/15), and Lucerne (LU04/14); these fish…

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Understanding Kfamscan

Understanding Kfamscan 0 I am doing functional prediction of bacteria, to do that I have a list of selected KO that are involved in the target functionality for example nitrogen fixation, phosphorous solubilization etc. First I obtain the KOs of my bacterial proteomes and do search for the KOs involved…

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KEGG COMPOUND: C00096

KEGG COMPOUND: C00096     COMPOUND: C00096 Help Entry C00096                      Compound                                Name GDP-mannose;GDP-D-mannose;GDP-alpha-D-mannose Formula C16H25N5O16P2 Exact mass 605.0772 Mol weight 605.3411 Structure Mol fileKCF fileDB search Remark Reaction Pathway map00051   Fructose and mannose metabolism map00053   Ascorbate and aldarate metabolism map00520   Amino sugar and nucleotide sugar metabolism map00541   O-Antigen nucleotide sugar biosynthesis map00571  …

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The evolutionary origin of host association in the Rickettsiales

Salje, J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat. Rev. Microbiol. 19, 375–390 (2021). CAS  PubMed  Article  Google Scholar  Wang, S. & Luo, H. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nat. Commun. 12, 3324 (2021). CAS  PubMed  PubMed Central  Article  Google Scholar  Strassert, J. F. H.,…

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Immune Infiltration and N(6)-Methyladenosine ncRNA Isoform Detection in Acute Lung Injury

Acute lung injury (ALI) is a severe form of sepsis that is associated with a high rate of morbidity and death in critically ill individuals. The emergence of ALI is the result of several factors at work. Case mortality rates might range from 40% to 70%. Researchers have discovered that…

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UniProt: A0A6I9ZUN5_ACIJB

ID A0A6I9ZUN5_ACIJB Unreviewed; 234 AA. AC A0A6I9ZUN5; DT 07-OCT-2020, integrated into UniProtKB/TrEMBL. DT 07-OCT-2020, sequence version 1. DT 25-MAY-2022, entry version 6. DE SubName: Full=tumor necrosis factor ligand superfamily member 8 {ECO:0000313|RefSeq:XP_014931799.1}; GN Name=TNFSF8 {ECO:0000313|RefSeq:XP_014931799.1}; OS Acinonyx jubatus (Cheetah). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Laurasiatheria;…

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Table 2 | Bioinformatics Strategies for the Analysis of Lipids

Systems information PATHWAY Pathway maps (16 reference pathway maps, including a lipid structure map for unsaturated fatty acids; classified in “Lipid Metabolism”) 93,644 BRITE Functional hierarchies (“Lipid Metabolism” in pathway and KEGG Orthology classification, and “Lipids” classification based on LIPIDMAPS) 15,687 MODULE Pathway modules (80 modules are defined for pathways…

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KEGG ENZYME: 1.14.19.32

Entry EC 1.14.19.32               Enzyme                                  Name palmitoyl-CoA 14-(E/Z)-desaturase Class Oxidoreductases;Acting on paired donors, with incorporation or reduction of molecular oxygen;With oxidation of a pair of donors resulting in the reduction of O2 to two molecules of waterBRITE hierarchy Sysname palmitoyl-CoA,ferrocytochrome b5:oxygen oxidoreductase (14,15 cis/trans-dehydrogenating) Reaction(IUBMB) (1) palmitoyl-CoA + 2 ferrocytochrome b5 + O2…

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KEGG ORTHOLOGY: K03191

KEGG ORTHOLOGY: K03191     ORTHOLOGY: K03191 Help Entry K03191                      KO                                      Symbol ureI Name acid-activated urea channel Pathway map05120   Epithelial cell signaling in Helicobacter pylori infection Brite KEGG Orthology (KO) [BR:ko00001] 09160 Human Diseases  09171 Infectious disease: bacterial   05120 Epithelial cell signaling in Helicobacter pylori infection    K03191  ureI; acid-activated urea channel 09180 Brite Hierarchies  09183 Protein families: signaling and…

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KEGG REACTION: R05288

Entry R05288                      Reaction                                Name p-xylene, ferredoxin:oxygen oxidoreductase (methyl-hydroxylating) Definition p-Xylene + Oxygen + 2 Reduced ferredoxin + 2 H+ <=> 4-Methylbenzyl alcohol + 2 Oxidized ferredoxin + H2O Equation Reaction class Enzyme Pathway rn01120   Microbial metabolism in diverse environments rn01220   Degradation of aromatic compounds Module M00537   Xylene degradation, xylene => methylbenzoate…

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KEGG COMPOUND: C07647

KEGG COMPOUND: C07647     COMPOUND: C07647 Help Entry C07647                      Compound                                Name Phosphoramide mustard;Phosphamide mustard Formula C4H11Cl2N2O2P Exact mass 219.9935 Mol weight 221.0221 Structure Mol fileKCF fileDB search Reaction Pathway map00982   Drug metabolism – cytochrome P450 Other DBs KCF data Show ATOM        11            1   N1c N    23.8758  -15.8550            2   P1a P    23.8642  -17.2548            3   C1b C    22.6627  -15.1552            4   C1b C    25.0830  -15.1611            5   N1a N    25.2698  -17.2548            6   O1c O    23.8583  -18.6603            7   O3b O    22.4645  -17.2548            8   C1b C    21.4497  -15.8550            9   C1b C    26.2963  -15.8610            10  X   Cl   20.2365  -15.1552            11  X   Cl   27.5093  -15.1728BOND        10            1     1   2 1            2     1   3…

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Pathway Enrichment

Pathway Enrichment 0 Is there any tool that can directly give me my gene id in first column and its pathway in second column? i am working with rice gene id. Thanks! KEGG ORA ENRICHMENT PATHWAY • 198 views • link updated 3 hours ago by newbio17 &utrif; 350 •…

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KEGG COMPOUND: C05172

Entry C05172                      Compound                                Name Selenophosphoric acid;Selenophosphate Formula H3PO3Se Exact mass 161.8985 Mol weight 160.9558 Structure Mol fileKCF fileDB search Reaction Pathway Enzyme Other DBs KCF data Show ATOM        5            1   P1b P    25.0600  -18.6200            2   O1c O    23.6600  -18.6200            3   O1c O    26.4600  -18.6200            4   O1c O    25.0600  -20.0200            5   Z   Se   25.0600  -17.2200BOND        4            1     1   2 1            2     1   3 1            3     1   4 2            4     1   5 1 Read more here: Source link

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Table_8_RNA-Seq and 16S rRNA Analysis Revealed the Effect of Deltamethrin on Channel Catfish in the Early Stage of Acute Exposure.xls

Deltamethrin (Del) is a widely used pyrethroid insecticide and a dangerous material that has brought serious problems to the healthy breeding of aquatic animals. However, the toxicological mechanisms of Del on channel catfish remain unclear. In the present study, we exposed channel catfish to 0, 0.5, and 5 μg/L Del…

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KEGG T01003: 286761

Entry 286761            CDS       T01003                                  Symbol Vcpip1 Name (RefSeq) deubiquitinating protein VCPIP1   KO K11861   deubiquitinating protein VCIP135 [EC:3.4.19.12] Organism rno  Rattus norvegicus (rat) Brite KEGG Orthology (KO) [BR:rno00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:rno01002]    286761 (Vcpip1)  09182 Protein families: genetic information processing   04121 Ubiquitin system [BR:rno04121]    286761 (Vcpip1)Enzymes [BR:rno01000] 3. Hydrolases  3.4  Acting on peptide bonds (peptidases)   3.4.19  Omega peptidases    3.4.19.12  ubiquitinyl…

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KEGG COMPOUND: C00311

KEGG COMPOUND: C00311     COMPOUND: C00311 Help Entry C00311                      Compound                                Name Isocitrate;Isocitric acid;1-Hydroxytricarballylic acid;1-Hydroxypropane-1,2,3-tricarboxylic acid Formula C6H8O7 Exact mass 192.027 Mol weight 192.1235 Structure Mol fileKCF fileDB search Reaction Pathway map00630   Glyoxylate and dicarboxylate metabolism map00720   Carbon fixation pathways in prokaryotes map01060   Biosynthesis of plant secondary metabolites map01061   Biosynthesis of phenylpropanoids…

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GitHub – ctlab/KEGG-network-pipeline

GitHub – ctlab/KEGG-network-pipeline This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another…

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KEGG ENZYME: 3.2.1.104

KEGG ENZYME: 3.2.1.104     ENZYME: 3.2.1.104 Help Entry EC 3.2.1.104                Enzyme                                  Name Class Hydrolases;Glycosylases;Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compoundsBRITE hierarchy Sysname cholesteryl-beta-D-glucoside glucohydrolase Reaction(IUBMB) cholesteryl-beta-D-glucoside + H2O = D-glucose + cholesterol [RN:R01460] Reaction(KEGG) Substrate Product Comment Acts on glucosides of cholesterol and sitosterol, but not on some related sterols…

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KEGG COMPOUND: C00399

KEGG COMPOUND: C00399     COMPOUND: C00399 Help Entry C00399                      Compound                                Name Ubiquinone;Coenzyme Q;CoQ;Q Formula C14H18O4(C5H8)n Structure Mol fileKCF fileDB search Comment Generic compound in reaction hierarchy n=5-9 Ubiquinone-6 [CPD:C17568] Ubiquinone-8 [CPD:C17569] Ubiquinone-9 [CPD:C01967] Ubiquinone-10 [CPD:C11378] [DR:D01065] Reaction Pathway Module M00142   NADH:ubiquinone oxidoreductase, mitochondria M00144   NADH:quinone oxidoreductase, prokaryotes M00145   NAD(P)H:quinone oxidoreductase, chloroplasts…

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KEGG ORTHOLOGY: K06625

Brite KEGG Orthology (KO) [BR:ko00001] 09130 Environmental Information Processing  09132 Signal transduction   04012 ErbB signaling pathway    K06625  CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A   04630 JAK-STAT signaling pathway    K06625  CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A   04066 HIF-1 signaling pathway    K06625  CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A   04068 FoxO signaling pathway    K06625  CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A   04151 PI3K-Akt signaling pathway    K06625  CDKN1A, P21,…

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KEGG COMPOUND: C05924

KEGG COMPOUND: C05924     COMPOUND: C05924 Help Entry C05924                      Compound                                Name Molybdopterin;Pyranopterin;H2Dtpp-mP Formula C10H14N5O6PS2 Exact mass 395.0123 Mol weight 395.3518 Structure Mol fileKCF fileDB search Reaction Pathway Module M00880   Molybdenum cofactor biosynthesis, GTP => molybdenum cofactor Enzyme Other DBs KCF data Show ATOM        24            1   S1a S    22.7500  -13.4003            2   S1a S    25.1308  -14.8087            3   C2y C    22.7383  -14.7666            4   C2y C    23.9353  -15.4866            5   C1y C    21.5555  -15.4809            6   C1y C    23.9236  -16.8776            7   C1y C    21.5496  -16.8718            8   N1x N    20.3269  -14.7608            9   C1b…

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MND1 Expression as a Predictor of Breast Cancer Survival

Introduction Breast cancer (BC) is the most commonly diagnosed cancer in women, and it is the main cause of cancer mortality in women around the world.1 Although standard treatments for breast cancer, including surgery, radiotherapy, chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, have greatly improved during the last few decades.2,3…

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Role of CD68 in tumor immunity and prognosis prediction in pan-cancer

Expression of CD68 in pan-cancer First, to fully clarify the expression of CD68 in pan-cancer, we matched the GTEx normal samples with TCGA tumor samples (Fig. 1A). We found that the levels of CD68 were significantly elevated (P < 0.01) in colon adenocarcinoma (COAD), glioblastoma multiforme (GBM), kidney renal clear cell carcinoma (KIRC),…

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Circulating cell-free mtDNA release is associated with the activation of cGAS-STING pathway and inflammation in mitochondrial diseases

Craven L, Alston C, Taylor R, Turnbull D (2017) Recent advances in mitochondrial disease. Annu Rev Genomics Hum Genet 18:257–275. doi.org/10.1146/annurev-genom-091416-035426 CAS  Article  PubMed  Google Scholar  El-Hattab AW, Adesina AM, Jones J, Scaglia F (2015) MELAS syndrome: clinical manifestations, pathogenesis, and treatment options. Mol Genet Metab 116(1–2):4–12. doi.org/10.1016/j.ymgme.2015.06.004 CAS  Article …

Continue Reading Circulating cell-free mtDNA release is associated with the activation of cGAS-STING pathway and inflammation in mitochondrial diseases

Differential Expression Profiles and Bioinformatics Analysis of tRNA-Derived Small RNAs in Muscle-Invasive Bladder Cancer in a Chinese Population

This article was originally published here Genes (Basel). 2022 Mar 28;13(4):601. doi: 10.3390/genes13040601. ABSTRACT Muscle-invasive bladder cancer (MIBC) leads to a large societal burden. Recently, tRNA-derived small RNAs (tsRNAs), a novel type of noncoding RNA (ncRNAs), have been identified. However, the expression patterns and functions of tsRNAs in MIBC have…

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KEGG COMPOUND: C05345

KEGG COMPOUND: C05345     COMPOUND: C05345 Help Entry C05345                      Compound                                Name beta-D-Fructose 6-phosphate;beta-D-Fructofuranose 6-phosphate Formula C6H13O9P Exact mass 260.0297 Mol weight 260.1358 Structure Mol fileKCF fileDB search Reaction Pathway map00010   Glycolysis / Gluconeogenesis map00051   Fructose and mannose metabolism map00520   Amino sugar and nucleotide sugar metabolism map00541   O-Antigen nucleotide sugar biosynthesis map00997  …

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Construction of a circRNA-Mediated ceRNA Network Reveals Novel Biomarkers for Aortic Dissection

Background: Aortic dissection (AD) is a rare and lethal disorder with its genetic basis remains largely unknown. Many studies have confirmed that circRNAs play important roles in various physiological and pathological processes. However, the roles of circRNAs in AD are still unclear and need further investigation. The present study aimed…

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KEGG MODULE: M00567

    MODULE: M00567 Help Entry M00567            Pathway   Module                                  Name Methanogenesis, CO2 => methane Definition (K00200+K00201+K00202+K00203-K11261+(K00205,K11260,K00204)) K00672 K01499 (K00319,K13942) K00320 (K00577+K00578+K00579+K00580+K00581-K00582-K00583+K00584) (K00399+K00401+K00402) (K22480+K22481+K22482,K03388+K03389+K03390,K08264+K08265,K03388+K03389+K03390+K14127+(K14126+K14128,K22516+K00125)) Diagram Orthology   4Fe-4S ferredoxin formylmethanofuran–tetrahydromethanopterin N-formyltransferase [EC:2.3.1.101] [RN:R03390] methenyltetrahydromethanopterin cyclohydrolase [EC:3.5.4.27] [RN:R03464] methylenetetrahydromethanopterin dehydrogenase [EC:1.5.99.9] [RN:R04456] 5,10-methenyltetrahydromethanopterin hydrogenase [EC:1.12.98.2] [RN:R04455] coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase [EC:1.5.99.11] [RN:R04464] Ortholog tableTaxonomyModule table…

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N6-methyladenosine modification of CENPK mRNA by ZC3H13 promotes cervical cancer stemness and chemoresistance | Military Medical Research

Bioinformatics analyses revealed the involvement of m6A modification in cervical cancer progression To better understand whether and how m6A regulators contribute to cervical cancer progression, we first identified 9 m6A writers (WTAP, ZC3H13, METTL3, METTL14, METTL16, VIRMA, RBM15B, RBM15, and CBLL1), 15 m6A readers (FMR1, hnRNPA2B1, hnRNPC, YTHDF1/2/3, YTHDC1/2, LRPPRC,…

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A hypoxia-related signature in lung squamous cell carcinoma

Introduction Lung cancer is the major leading cause of tumour-related deaths throughout the world, while lung squamous cell carcinoma (LUSC) as the second most common histological type of lung cancer.1 Each year, almost 1.8 million people are diagnosed with lung cancer worldwide and 400,000 of these die from LUSC.2,3 Due to…

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Bioconductor – keggorthology

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see keggorthology. graph support for KO, KEGG Orthology Bioconductor version: 2.13 graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused…

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Bioconductor – neaGUI

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see neaGUI. An R package to perform the network enrichment analysis (NEA). Bioconductor version: 2.13 neaGUI is an easy to use R package developed to perform the network enrichment analysis (NEA) proposed by Alexeyenko…

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Bioinformatics analysis identifies widely expressed genes

1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…

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A multi-omics approach to elucidate the mechanisms of action of a dietary muramidase administered to broiler chickens

Gadde, U., Kim, W. H., Oh, S. T. & Lillehoj, H. S. Alternatives to antibiotics for maximizing growth performance and feed efficiency in poultry: a review. Animal Health Res. Rev. 18, 26–45 (2017). CAS  Google Scholar  Smits, C. H. M., Li, D., Patience, J. F. & den Hartog, L. A….

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Metagenomic data-analysis reveals enrichment of lipopolysaccharide synthesis in the gut microbiota of atrial fibrillation patients

This article was originally published here Zhonghua Xin Xue Guan Bing Za Zhi. 2022 Mar 24;50(3):249-256. doi: 10.3760/cma.j.cn112148-20210106-00015. ABSTRACT Objective: To investigate the functional changes of key gut microbiota (GM) that produce lipopolysaccharide (LPS) in atrial fibrillation (AF) patients and to explore their potential role in the pathogenesis of AF….

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KEGG COMPOUND: C01380

Entry C01380                      Compound                                Name Ethylene glycol;1,2-Ethanediol;Ethane-1,2-diol Formula C2H6O2 Exact mass 62.0368 Mol weight 62.0678 Structure Mol fileKCF fileDB search Reaction Pathway map00625   Chloroalkane and chloroalkene degradation map00630   Glyoxylate and dicarboxylate metabolism map01120   Microbial metabolism in diverse environments Enzyme Other DBs KCF data Show ATOM        4            1   C1b C    28.1392  -16.3327            2   C1b C    29.5408  -16.3327            3   O1a O    27.4444  -17.5473            4   O1a O    30.2356  -17.5473BOND        3            1     1   2 1            2     1   3 1            3     2   4 1…

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Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis

Rawla, P., Sunkara, T., Muralidharan, P. & Raj, J. P. Update in global trends and aetiology of hepatocellular carcinoma. Contemp. Oncol. (Poznan, Poland) 22, 141–150 (2018). CAS  Google Scholar  Kong, D. et al. Current statuses of molecular targeted and immune checkpoint therapies in hepatocellular carcinoma. Am. J. Cancer Res. 10,…

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KEGG REACTION: R01627

KEGG REACTION: R01627     REACTION: R01627 Help Entry R01627                      Reaction                                Name 3-dehydroshikimate hydro-lyase Definition 3-Dehydroshikimate <=> 3,4-Dihydroxybenzoate + H2O Equation Reaction class Enzyme Pathway rn01053   Biosynthesis of siderophore group nonribosomal peptides rn01110   Biosynthesis of secondary metabolites Orthology Other DBs LinkDB All DBs DBGET integrated database retrieval system Read more here: Source…

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KEGG COMPOUND: C02538

KEGG COMPOUND: C02538     COMPOUND: C02538 Help Entry C02538                      Compound                                Name Formula C18H22O5S Exact mass 350.1188 Mol weight 350.4293 Structure Mol fileKCF fileDB search Reaction Pathway map00140   Steroid hormone biosynthesis Enzyme Brite Compounds with biological roles [BR:br08001] Hormones and transmitters  Steroid hormones   Estrogens    C02538  Estrone 3-sulfateLipids [BR:br08002] ST  Sterol lipids  ST02 Steroids   ST0201 C18 steroids (estrogens) and derivatives    C02538  Estrone 3-sulfate  ST05 Steroid…

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Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation

Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…

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Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis

Hallam, S. J., Goncharov, A., McEwen, J., Baran, R. & Jin, Y. Syd-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains specifies axon identity in C. elegans. Nat. Neurosci. 5, 1137–1146 (2002). CAS  PubMed  Google Scholar  Xu, Y. & Quinn, C. C. SYD-1 promotes multiple developmental steps leading to…

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KEGG ORTHOLOGY: K13942

KEGG ORTHOLOGY: K13942     ORTHOLOGY: K13942 Help Entry K13942                      KO                                      Symbol hmd Name 5,10-methenyltetrahydromethanopterin hydrogenase [EC:1.12.98.2] Pathway map01120   Microbial metabolism in diverse environments Module M00567   Methanogenesis, CO2 => methane Brite KEGG Orthology (KO) [BR:ko00001] 09100 Metabolism  09102 Energy metabolism   00680 Methane metabolism    K13942  hmd; 5,10-methenyltetrahydromethanopterin hydrogenaseEnzymes [BR:ko01000] 1. Oxidoreductases  1.12  Acting on hydrogen as donor   1.12.98  With other, known, physiological acceptors    1.12.98.2  5,10-methenyltetrahydromethanopterin…

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Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

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Identification of Hub Genes Associated with COPD Through Integrated Bi

Introduction Chronic obstructive pulmonary disease (COPD) will become the third leading cause of death worldwide.1,2 The incidence of COPD worldwide is 13.1%3 and is 13.7% in the Chinese population over 40 years of age.4 Emphysema is one of the most common phenotypes.1 Over the past few decades, we have conducted…

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KEGG COMPOUND: C01113

KEGG COMPOUND: C01113     COMPOUND: C01113 Help Entry C01113                      Compound                                Name D-Galactose 6-phosphate;6-Phospho-D-galactose Formula C6H13O9P Exact mass 260.0297 Mol weight 260.1358 Structure Mol fileKCF fileDB search Reaction Pathway map02060   Phosphotransferase system (PTS) Enzyme Other DBs KCF data Show ATOM        16            1   P1b P    25.9015  -16.0011            2   O2b O    27.3009  -16.0070            3   O1c O    25.8898  -17.4005            4   O1c O    24.5021  -16.0011            5   O1c O    25.8898  -14.6076            6   C1b C    28.3679  -15.0973            7   C1y C    29.5748  -15.8029            8   C1y C    29.5748  -17.2021            9   O2x O    30.7818  -15.0973            10  C1y C    30.7818  -17.9018            11  O1a O    28.3679  -17.9018            12  C1y C    32.0005  -15.8029            13  C1y…

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KEGG COMPOUND: C00469

KEGG COMPOUND: C00469     COMPOUND: C00469 Help Entry C00469                      Compound                                Name Ethanol;Ethyl alcohol;Methylcarbinol Formula C2H6O Exact mass 46.0419 Mol weight 46.0684 Structure Mol fileKCF fileDB search Remark Reaction Pathway map00010   Glycolysis / Gluconeogenesis map01110   Biosynthesis of secondary metabolites map01120   Microbial metabolism in diverse environments map04750   Inflammatory mediator regulation of TRP channels…

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KEGG T01001: 5105

Entry 5106              CDS       T01001                                  Symbol PCK2, PEPCK, PEPCK-M, PEPCK2 Name (RefSeq) phosphoenolpyruvate carboxykinase 2, mitochondrial   KO K01596   phosphoenolpyruvate carboxykinase (GTP) [EC:4.1.1.32] Organism hsa  Homo sapiens (human) Pathway hsa00010   Glycolysis / Gluconeogenesis hsa00020   Citrate cycle (TCA cycle) hsa00620   Pyruvate metabolism hsa01100   Metabolic pathways hsa03320   PPAR signaling pathway hsa04068   FoxO signaling pathway hsa04151   PI3K-Akt signaling…

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KEGG COMPOUND: C00565

Entry C00565                      Compound                                Name Trimethylamine;(CH3)3N;N,N-Dimethylmethanamine Formula C3H9N Exact mass 59.0735 Mol weight 59.1103 Structure Mol fileKCF fileDB search Reaction Pathway map01120   Microbial metabolism in diverse environments Module M00563   Methanogenesis, methylamine/dimethylamine/trimethylamine => methane Enzyme Other DBs KCF data Show ATOM        4            1   N1c N    22.1200  -15.8200            2   C1a C    23.3299  -15.1185            3   C1a C    20.9101  -15.1185            4   C1a C    22.1200  -17.2929BOND        3            1     1   2 1            2     1   3 1            3     1   4 1 Read more here: Source link

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Workflow Platforms for Systems Genetics

Workflow Platforms for Systems Genetics eQTL Platforms eQTL Viewer Mouse Genome Informatics: Phenotypes, Alleles & Disease Models PhenoGen Informatics (CO U) eXtensible Genotype And Phenotype platform (XGAP) MOLGENIS & MetaNetwork, Swertz & Jansen, U Groningen Weighted Gene Co-expression Network Analysis (WGCNA), Horvath, UCLA iPlant Sage Bionetworks Repository: Synapse GenomeSpace Institute…

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KEGG ENZYME: 2.7.2.1

Entry EC 2.7.2.1                  Enzyme                                  Name acetate kinase;acetokinase;AckA;AK;acetic kinase;acetate kinase (phosphorylating) Class Transferases;Transferring phosphorus-containing groups;Phosphotransferases with a carboxy group as acceptorBRITE hierarchy Sysname ATP:acetate phosphotransferase Reaction(IUBMB) ATP + acetate = ADP + acetyl phosphate [RN:R00315] Reaction(KEGG) Substrate Product Comment Requires Mg2+ for activity. While purified enzyme from Escherichia coli is specific for acetate…

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KEGG COMPOUND: C00247

KEGG COMPOUND: C00247     COMPOUND: C00247 Help Entry C00247                      Compound                                Name L-Sorbose;L-xylo-Hexulose Formula C6H12O6 Exact mass 180.0634 Mol weight 180.1559 Structure Mol fileKCF fileDB search Comment Reaction Pathway map00051   Fructose and mannose metabolism Enzyme Brite Compounds with biological roles [BR:br08001] Carbohydrates  Monosaccharides   Ketoses    C00247  L-Sorbose BRITE hierarchy Other DBs KCF data Show ATOM        12            1   C1z C    26.2968  -14.4371            2   C1y C    26.2968  -15.8376            3   O2x O    25.0888  -13.7368            4   C1b…

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Exosomal microRNA-618 derived from mesenchymal stem cells attenuate the progression of hepatic fibrosis by targeting Smad4

Introduction Hepatic fibrosis (HF) is a pathological phenomenon produced in the process of long-term damage and repair in the liver [1,2]. During the formation of HF, hepatocytes are damaged by various factors, such as chronic liver disease, and excessive intake of alcohol, and secrete a variety of cytokines [3]. Subsequently,…

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Comprehensive bioinformatics analysis reveals the hub genes and pathways associated with multiple myeloma

This article was originally published here Hematology. 2022 Dec;27(1):280-292. doi: 10.1080/16078454.2022.2040123. ABSTRACT PURPOSE: While the prognosis of multiple myeloma (MM) has significantly improved over the last decade because of new treatment options, it remains incurable. Aetiological explanations and biological targets based on genomics may provide additional help for rational disease…

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Validation of hub genes in acute pancreatitis

Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…

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KEGG COMPOUND: C21620

KEGG COMPOUND: C21620     COMPOUND: C21620 Help Entry C21620                      Compound                                Name S-[(E)-N-Hydroxy(indol-3-yl)acetimidoyl]-L-glutathione Formula C20H25N5O7S Exact mass 479.1475 Mol weight 479.5068 Structure Mol fileKCF fileDB search Reaction Enzyme Other DBs KCF data Show ATOM        33            1   C8y C    17.0403  -15.7134            2   C8y C    18.3672  -15.9928            3   C8y C    16.3420  -16.9006            4   C8x C    16.3420  -14.4564            5   C8x C    18.4371  -17.3895            6   N4x N    17.1800  -17.9482            7   C8x C    14.8754  -16.9006            8   C8x C    14.9452  -14.4564            9   C8x C    14.1770  -15.7134            10  O1b O    19.6829  -18.0281            11  N2b N    20.8589  -17.2684            12  C2c C    20.7891  -15.8717            13  C1b C    19.5432  -15.2331            14  C1b C    23.2109  -15.7506            15  S2a S    21.9650  -15.1120            16  C1c C    24.3869  -14.9909            17  N1b N    24.3170  -13.5927            18  C5a C    25.6328  -15.6295            19  O5a…

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Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

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Fatty infiltration after rotator cuff tear

Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…

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KEGG T03334: R50912_07385

Entry R50912_23945      CDS       T03334                                  Name (GenBank) alpha-galactosidase   KO K07407   alpha-galactosidase [EC:3.2.1.22] Organism paeq  Paenibacillus sp. FSL R5-0912 Pathway paeq00052   Galactose metabolism paeq00561   Glycerolipid metabolism paeq00600   Sphingolipid metabolism paeq01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:paeq00001] 09100 Metabolism  09101 Carbohydrate metabolism   00052 Galactose metabolism    R50912_23945  09103 Lipid metabolism   00561 Glycerolipid metabolism    R50912_23945   00600 Sphingolipid metabolism    R50912_23945Enzymes [BR:paeq01000] 3. Hydrolases  3.2  Glycosylases   3.2.1  Glycosidases, i.e. enzymes that hydrolyse O-…

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KEGG ENZYME: 2.4.1.81

Entry EC 2.4.1.81                 Enzyme                                  Name flavone 7-O-beta-glucosyltransferase;UDP-glucose-apigenin beta-glucosyltransferase;UDP-glucose-luteolin beta-D-glucosyltransferase;uridine diphosphoglucose-luteolin glucosyltransferase;uridine diphosphoglucose-apigenin 7-O-glucosyltransferase;UDP-glucosyltransferase (ambiguous) Class Transferases;Glycosyltransferases;HexosyltransferasesBRITE hierarchy Sysname UDP-glucose:5,7,3′,4′-tetrahydroxyflavone 7-O-beta-D-glucosyltransferase Reaction(IUBMB) UDP-glucose + 5,7,3′,4′-tetrahydroxyflavone = UDP + 7-O-beta-D-glucosyl-5,7,3′,4′-tetrahydroxyflavone [RN:R03588] Reaction(KEGG) Substrate UDP-glucose [CPD:C00029]; 5,7,3′,4′-tetrahydroxyflavone [CPD:C01514] Product UDP [CPD:C00015]; 7-O-beta-D-glucosyl-5,7,3′,4′-tetrahydroxyflavone [CPD:C03951] Comment A number of flavones, flavanones and flavonols can function as acceptors….

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KEGG REACTION: R02703

KEGG REACTION: R02703     REACTION: R02703 Help Entry R02703                      Reaction                                Name D-Mannitol-1-phosphate:NAD+ 5-oxidoreductase Definition D-Mannitol 1-phosphate + NAD+ <=> beta-D-Fructose 6-phosphate + NADH + H+ Equation Reaction class Enzyme Pathway rn00051   Fructose and mannose metabolism Orthology LinkDB All DBs DBGET integrated database retrieval system Read more here: Source link

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KEGG ENZYME: 2.2.1.4

KEGG ENZYME: 2.2.1.4     ENZYME: 2.2.1.4 Help Entry EC 2.2.1.4                  Enzyme                                  Name acetoin—ribose-5-phosphate transaldolase;1-deoxy-D-altro-heptulose-7-phosphate synthetase;1-deoxy-D-altro-heptulose-7-phosphate synthase;3-hydroxybutan-2-one:D-ribose-5-phosphate aldehydetransferase [wrong substrate name] Class Transferases;Transferring aldehyde or ketonic groups;Transketolases and transaldolasesBRITE hierarchy Sysname 3-hydroxybutan-2-one:D-ribose-5-phosphate aldehydetransferase Reaction(IUBMB) 3-hydroxybutan-2-one + D-ribose 5-phosphate = acetaldehyde + 1-deoxy-D-altro-heptulose 7-phosphate [RN:R02345] Reaction(KEGG) Substrate 3-hydroxybutan-2-one [CPD:C00466]; D-ribose 5-phosphate [CPD:C00117] Product acetaldehyde…

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KEGG REACTION: R03385

KEGG REACTION: R03385     REACTION: R03385 Help Entry R03385                      Reaction                                Name 3-hydroxy-2-methylpyridine-5-carboxylate,NADH:oxygen oxidoreductase (ring-opening) Definition 3-Hydroxy-2-methylpyridine-5-carboxylate + Oxygen + NADH + H+ <=> 2-(Acetamidomethylene)succinate + NAD+ Equation Comment Reaction class Enzyme Pathway rn01120   Microbial metabolism in diverse environments Orthology Other DBs LinkDB All DBs DBGET integrated database retrieval system Read more…

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KEGG COMPOUND: C06070

KEGG COMPOUND: C06070     COMPOUND: C06070 Help Entry C06070                      Compound                                Name Iridotrial;(1S,2R,3S)-2-Formyl-alpha-(hydroxymethylene)-3-methylcyclopentaneacetaldehyde Formula C10H14O3 Exact mass 182.0943 Mol weight 182.2164 Structure Mol fileKCF fileDB search Reaction Pathway map01110   Biosynthesis of secondary metabolites Enzyme Brite Lipids [BR:br08002] PR  Prenol lipids  PR01 Isoprenoids   PR0102 C10 isoprenoids (monoterpenes)    PR010207 Iridoid, 10-alkyliridoid and secoiridoid monoterpenoids     C06070  IridotrialPhytochemical compounds [BR:br08003] Terpenoids  Monoterpenoids (C10)   Iridoids    C06070  Iridotrial BRITE hierarchy…

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Comprehensive circRNA Analyses in Human Vertebrae of GIOP and Its Molecular Mechanism

Circular RNAs (circRNAs) are a novel class of noncoding RNAs that play important roles in human diseases. However, the regulation of circRNAs in glucocorticoid-induced osteoporosis (GIOP) has not been reported. In this study, we performed high-throughput sequencing to identify altered circRNAs in the vertebrae from GIOP patients. A total of…

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Identification of a four-gene signature & PTC.

Introduction Thyroid carcinoma (THCA) is the most common type of endocrine malignancy and its incidence is increasing.1 Based on its histopathological characteristics, thyroid carcinoma can be classified into multiple subtypes, such as papillary thyroid carcinoma (PTC), follicular thyroid carcinoma, and anaplastic thyroid carcinoma.2 PTC is the most common subtype of…

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How to do functional analysis on differentially expressed gene list from RNA-seq data?

How to do functional analysis on differentially expressed gene list from RNA-seq data? 0 @06f08eeb Last seen 1 day ago Canada Hi all, I am a complete beginner in terms of bioinformatics analysis and I am hoping to complete some functional analysis on some differentially expressed gene lists of some…

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KEGG REACTION: R00481

KEGG REACTION: R00481     REACTION: R00481 Help Entry R00481                      Reaction                                Name L-aspartate:oxygen oxidoreductase Definition L-Aspartate + Oxygen <=> Iminoaspartate + Hydrogen peroxide Equation Comment Reaction class Enzyme Pathway rn00760   Nicotinate and nicotinamide metabolism rn01240   Biosynthesis of cofactors Module M00115   NAD biosynthesis, aspartate => quinolinate => NAD Orthology Other DBs LinkDB All…

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Novel diagnostic biomarkers for keloid based on GEO database

Introduction Keloid is excessive fibrosis of the skin that extends beyond the area of injury and does not regress.1 Keloid can occur in the joints and mouth after several years of severe injury, including burns, chemical injury, wound, and surgical incision.2 Keloids on the joints affect the quality of life,…

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KEGG T00007: b1542

Entry b4323             CDS       T00007                                  Symbol uxuB Name (RefSeq) D-mannonate oxidoreductase   KO K00040   fructuronate reductase [EC:1.1.1.57] Organism eco  Escherichia coli K-12 MG1655 Pathway eco00040   Pentose and glucuronate interconversions eco01100   Metabolic pathways Module eco_M00061   D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P Brite KEGG Orthology (KO) [BR:eco00001] 09100 Metabolism  09101 Carbohydrate metabolism   00040 Pentose and glucuronate interconversions    b4323 (uxuB)Enzymes…

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KEGG REACTION: R00226

Entry R00226                      Reaction                                Name pyruvate:pyruvate acetaldehydetransferase (decarboxylating);(S)-2-acetolactate pyruvate-lyase (carboxylating) Definition (S)-2-Acetolactate + CO2 <=> 2 Pyruvate Equation Comment Reaction class Enzyme Pathway rn00290   Valine, leucine and isoleucine biosynthesis rn00660   C5-Branched dibasic acid metabolism rn00770   Pantothenate and CoA biosynthesis rn01110   Biosynthesis of secondary metabolites rn01210   2-Oxocarboxylic acid metabolism rn01230   Biosynthesis of amino…

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Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells

Aghamohseni H, Ohadi K, Spearman M, Krahn N, Moo-Young M, Scharer JM, Butler M, Budman HM (2014) Effects of nutrient levels and average culture pH on the glycosylation pattern of camelid-humanized monoclonal antibody. J Biotechnol 186:98–109. doi.org/10.1016/j.jbiotec.2014.05.024 CAS  Article  PubMed  Google Scholar  Altamirano C, Illanes A, Casablancas A, Gámez X,…

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KEGG ENZYME: 3.1.3.96

Entry EC 3.1.3.96                 Enzyme                                  Name pseudouridine 5′-phosphatase;pseudouridine 5′-monophosphatase;5′-PsiMPase;HDHD1 Class Hydrolases;Acting on ester bonds;Phosphoric-monoester hydrolasesBRITE hierarchy Sysname pseudouridine 5′-phosphohydrolase Reaction(IUBMB) pseudouridine 5′-phosphate + H2O = pseudouridine + phosphate [RN:R11180] Reaction(KEGG) R11180 Reaction Substrate pseudouridine 5′-phosphate [CPD:C01168]; H2O [CPD:C00001] Product pseudouridine [CPD:C02067]; phosphate [CPD:C00009] Comment Requires Mg2+ for activity. History EC 3.1.3.96 created 2014…

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KEGG REACTION: R03197

    REACTION: R03197 Help Entry R03197                      Reaction                                Name Uroporphyrinogen-III carboxy-lyase Definition Uroporphyrinogen III <=> Coproporphyrinogen III + 4 CO2 Equation Reaction class Enzyme Pathway rn01110   Biosynthesis of secondary metabolites rn01240   Biosynthesis of cofactors Module M00121   Heme biosynthesis, plants and bacteria, glutamate => heme M00868   Heme biosynthesis, animals and fungi, glycine =>…

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KEGG PATHWAY: map00051

Entry map00051                    Pathway                                 Name Fructose and mannose metabolism Class Metabolism; Carbohydrate metabolismBRITE hierarchy Pathway map map00051   Fructose and mannose metabolism Ortholog table Module M00114   Ascorbate biosynthesis, plants, fructose-6P => ascorbate [PATH:map00051] Other DBs Relatedpathway map00010   Glycolysis / Gluconeogenesis map00053   Ascorbate and aldarate metabolism map00520   Amino sugar and nucleotide sugar metabolism KO pathway Read…

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KEGG ENZYME: 6.5.1.9

Entry EC 6.5.1.9                  Enzyme                                  Name cyclic 2,3-diphosphoglycerate synthase;cpgS (gene name) Class Ligases;Forming phosphoric-ester bonds;Ligases that form phosphoric-ester bonds (only sub-subclass identified to date)BRITE hierarchy Sysname (2R)-2,3-bisphosphoglycerate ligase (cyclizing) Reaction(IUBMB) ATP + 2,3-diphospho-D-glycerate = ADP + phosphate + cyclic 2,3-bisphosphoglycerate [RN:R03298] Reaction(KEGG) Substrate Product Comment The enzyme is present in a number of…

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Immune-related Prognostic Genes of ccRCC

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

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KEGG REACTION: R00750

Entry R00750                      Reaction                                Name 4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming) Definition Acetaldehyde + Pyruvate <=> 4-Hydroxy-2-oxopentanoate Equation Reaction class Enzyme Pathway rn00360   Phenylalanine metabolism rn01120   Microbial metabolism in diverse environments rn01220   Degradation of aromatic compounds Module M00545   Trans-cinnamate degradation, trans-cinnamate => acetyl-CoA M00569   Catechol meta-cleavage, catechol => acetyl-CoA / 4-methylcatechol => propanoyl-CoA Orthology Other…

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